Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Micro-PVM"

graph_weight

## [1] "1.0"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   32.00   36.75   38.00   37.58   39.00   42.00

length(n_genes)

## [1] 40

sort(n_genes)

##  [1] 32 33 34 34 35 35 36 36 36 36 37 37 37 37 37 37 37 37 37 38 38 38 38 38 38
## [26] 38 38 38 39 39 39 40 40 40 40 40 40 41 41 42

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1739   261

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1718   261

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "SYT7"          "CDH20"         "NALCN"         "ARFGEF3"      
##  [5] "ADAM23"        "DNAH6"         "CHD5"          "CSMD2"        
##  [9] "PCSK2"         "ATP8A2"        "CBLN2"         "STXBP5L"      
## [13] "TENM2"         "CNTN5"         "ZNF385D"       "AK5"          
## [17] "CLSTN2"        "ANKRD30BL"     "RANBP3L"       "ADGRV1"       
## [21] "AMER2"         "GREM1"         "FSTL5"         "FUT9"         
## [25] "HPSE2"         "SRRM3"         "SSTR2"         "FLRT2"        
## [29] "CACNA1E"       "LINC00632"     "BASP1-AS1"     "ROR1-AS1"     
## [33] "RP11-191L9.4"  "AC093843.1"    "LINC01435"     "RP11-384F7.2" 
## [37] "CTC-340A15.2"  "SLC5A4-AS1"    "CTC-535M15.2"  "RMST"         
## [41] "RP11-436D23.1"
## [1] "found 29 genes."

## [1] 2
##  [1] "PDK4"          "ABCB4"         "CPED1"         "GASK1A"       
##  [5] "SESN3"         "TENM4"         "GASK1B"        "FOLR2"        
##  [9] "ARHGAP42"      "PLD4"          "CYSLTR1"       "C5orf64"      
## [13] "RAB39A"        "CLEC9A"        "MAMDC2-AS1"    "AC003090.1"   
## [17] "LMCD1-AS1"     "HDAC2-AS2"     "LINC02642"     "RP11-634B7.4" 
## [21] "COX10-AS1"     "AC008697.1"    "LINC01301"     "LINC01094"    
## [25] "MAILR"         "MIR3142HG"     "RP11-946L16.1" "RP11-554D14.6"
## [29] "RP11-187O7.3"  "MRC1"          "MIR222HG"      "MIR223HG"     
## [33] "LINC00506"     "RP11-323F24.5" "RP11-685G11.1" "RP11-4F5.3"   
## [37] "CPM"           "KCNE1"        
## [1] "found 16 genes."

## [1] 3
##  [1] "SIGLEC1"       "ADGRD1"        "F13A1"         "LILRB2"       
##  [5] "ENOSF1"        "IFI44L"        "CH25H"         "FHAD1"        
##  [9] "TMEM163"       "ADAMTS15"      "PGBD5"         "ODF3B"        
## [13] "PLCXD3"        "MS4A4E"        "RP11-445F6.2"  "LINC01515"    
## [17] "AC092431.3"    "LINC02008"     "BDNF-AS"       "LINC02211"    
## [21] "LINC02432"     "C5orf17"       "LINC02196"     "FAM66D"       
## [25] "OVCH1-AS1"     "RP11-72M17.1"  "CTD-2336H13.2" "LINC02073"    
## [29] "RP11-154H12.3" "RP11-354K4.2"  "CCDC28A-AS1"   "LINC01374"    
## [33] "RP11-281A20.2" "CERNA2"        "RP11-221G19.1" "RP11-321P16.3"
## [37] "RP13-52K8.2"  
## [1] "found 14 genes."

## [1] 4
##  [1] "ACER3"         "CARMIL1"       "SYNDIG1"       "FAM149A"      
##  [5] "TBC1D14"       "NPL"           "NKD1"          "AOPEP"        
##  [9] "DISP1"         "SAMSN1"        "DEPTOR"        "DENND2B"      
## [13] "ATF7IP2"       "TMC7"          "SPTLC3"        "SCAI"         
## [17] "ZDHHC14"       "KCNQ3"         "PRKN"          "RANBP17"      
## [21] "LINC02649"     "MIR99AHG"      "RP1-30E17.2"   "HMGA1P4"      
## [25] "ZFPM2-AS1"     "RP11-10H3.1"   "RP11-692P14.1" "RP6-91H8.6"   
## [29] "ARHGAP6"       "KCNQ2"         "RAP1GAP"       "PILRA"        
## [33] "GRK3"          "PADI2"         "SEC14L1"       "SLC2A13"      
## [37] "KCNQ5"         "LNCAROD"      
## [1] "found 29 genes."

## [1] 5
##  [1] "MGLL"          "PRTFDC1"       "NIPAL2"        "MAP2K6"       
##  [5] "IFT43"         "CCDC18"        "SSPN"          "GSTCD"        
##  [9] "MED12L"        "FILIP1L"       "GPR34"         "CENPP"        
## [13] "RP5-1132H15.1" "RMDN2-AS1"     "RP11-692D12.1" "LINC00624"    
## [17] "HGF"           "TGFB2"         "TMED8"         "CLNK"         
## [21] "HPCAL1"        "TOX2"          "TMEM115"       "GYPC"         
## [25] "FAM117B"       "CCDC40"        "IQGAP2"        "HTR7"         
## [29] "PARP8"         "PCNT"          "RHOBTB3"       "ABCA1"        
## [33] "GLRX"          "GOLIM4"        "EFCAB2"        "SLC48A1"      
## [37] "SBF2-AS1"      "RP11-154H23.4"
## [1] "found 32 genes."

## [1] 6
##  [1] "HHAT"       "ZNF821"     "MOBP"       "AATK"       "ST3GAL1"   
##  [6] "FAM50A"     "RGS1"       "MTMR8"      "ADAP1"      "MEGF9"     
## [11] "SNX25"      "DARS1"      "CDH26"      "SEM1"       "AFDN"      
## [16] "KIAA0513"   "GPNMB"      "CCNG2"      "ARHGAP18"   "TIAM2"     
## [21] "RSU1"       "FRRS1"      "ABCG1"      "ANKZF1"     "MARCHF8"   
## [26] "APLF"       "MFSD4B"     "ZC3H6"      "DPYD"       "PARVB"     
## [31] "H1-0"       "CYRIA"      "GCC2-AS1"   "AC093818.1" "PIK3IP1-DT"
## [36] "MIR181A1HG" "IFITM10"    "CLEC5A"    
## [1] "found 34 genes."

## [1] 7
##  [1] "SLC4A7"   "EPB41L2"  "POLA1"    "TGFBR1"   "SIPA1L2"  "BIN1"    
##  [7] "BACH1"    "SOCS6"    "SH3RF3"   "FNDC3B"   "TRIP11"   "TJP1"    
## [13] "ARHGEF10" "DDX5"     "GAB1"     "E2F3"     "P4HA1"    "RASSF8"  
## [19] "RUNX2"    "ARHGAP22" "UACA"     "FNBP1L"   "MSN"      "MCPH1"   
## [25] "MGAT5"    "RUNX1"    "ZNF143"   "AXL"      "LDLRAD4"  "ALCAM"   
## [31] "PEAK1"    "SND1"    
## [1] "found 32 genes."

## [1] 8
##  [1] "PDE10A"        "GNLY"          "ADAMTS19"      "GLT1D1"       
##  [5] "BANK1"         "ADAMTS3"       "UCN"           "MT1E"         
##  [9] "TMEM151B"      "RFLNA"         "ZNF804B"       "LINC01277"    
## [13] "AC073115.7"    "AC002539.1"    "RP3-525N10.2"  "LINC00271"    
## [17] "KIF5C-AS1"     "LINC02884"     "AC007682.1"    "AC073115.6"   
## [21] "MIR4300HG"     "STARD4-AS1"    "LINC00923"     "LINC02055"    
## [25] "RP4-809F18.1"  "MTRNR2L8"      "LINC02316"     "PSMD7-DT"     
## [29] "RP11-621L6.2"  "RP11-58G13.1"  "RP11-413N10.3" "RP11-640F22.1"
## [33] "LINC02885"     "RP11-38B6.1"   "RP11-320L2.1"  "RP11-341N18.1"
## [1] "found 12 genes."

## [1] 9
##  [1] "HTR2B"     "PNMA3"     "ZNRF1"     "NFIX"      "NSMAF"     "PDE8A"    
##  [7] "GRAMD4"    "FOSL2"     "TBC1D2"    "PCSK5"     "RNF24"     "BNIP3L"   
## [13] "GYS1"      "PPARD"     "PFKFB4"    "GBE1"      "PAPOLG"    "NR4A3"    
## [19] "ATF1"      "KDM6B"     "PHF21A"    "GLUL"      "GABARAPL1" "PELI2"    
## [25] "GNA12"     "SLC25A37"  "ARID5B"    "CFDP1"     "MAPK13"    "SPRY1"    
## [31] "NFIL3"     "PPIP5K1"   "KLHL6"     "PPP1R3B"   "BNIP3"     "TRNAU1AP" 
## [37] "LIMK2"    
## [1] "found 37 genes."

## [1] 10
##  [1] "SCMH1"                   "KIFAP3"                 
##  [3] "APBB1IP"                 "TMEM156"                
##  [5] "SPATA6"                  "FRMD6"                  
##  [7] "KCNMB1"                  "RASGEF1C"               
##  [9] "KCNMA1"                  "AUTS2"                  
## [11] "TAGAP"                   "TMEM52B"                
## [13] "NAV2"                    "ZNF608"                 
## [15] "TLN2"                    "GAP43"                  
## [17] "OLR1"                    "DLEU1"                  
## [19] "B3GNT5"                  "NCKAP5"                 
## [21] "SPATA13_ENSG00000182957" "SLC8A1"                 
## [23] "SFMBT2"                  "MBD5"                   
## [25] "TMSB4X"                  "LTC4S"                  
## [27] "RP11-557H15.4"           "LINC02232"              
## [29] "RP11-419I17.1"           "RNASET2"                
## [31] "RGCC"                    "ZBTB46"                 
## [33] "PCGF5"                   "FMN1"                   
## [1] "found 29 genes."

## [1] 11
##  [1] "MUSK"                      "EFR3B"                    
##  [3] "PROCR"                     "CRYM"                     
##  [5] "STMN2"                     "ECM2"                     
##  [7] "OPRM1"                     "PODXL2"                   
##  [9] "NEK11"                     "WLS"                      
## [11] "IFIT3"                     "IFIT2"                    
## [13] "FMO5"                      "ABCA8"                    
## [15] "MMS22L"                    "IER2"                     
## [17] "FAM227B"                   "BEAN1"                    
## [19] "GLYATL1"                   "MYO5B"                    
## [21] "SLC35G2"                   "CPLX1"                    
## [23] "DTWD2"                     "DENND5B"                  
## [25] "GRIK1"                     "PC"                       
## [27] "MCMDC2"                    "TSPYL2"                   
## [29] "IFIT1"                     "STMN3"                    
## [31] "H2BC18"                    "SMCR5"                    
## [33] "GPRC5D-AS1"                "LINC01605_ENSG00000253161"
## [35] "RP11-867G2.8"              "RP11-314L11.1"            
## [37] "TMEM140"                  
## [1] "found 32 genes."

## [1] 12
##  [1] "PLPP1"          "HAMP"           "AZIN2"          "SHOC1"         
##  [5] "NLGN4Y"         "MICOS10"        "ADGRG2"         "TTTY14"        
##  [9] "FLJ40194"       "DLEU7"          "COL25A1"        "EDNRB-AS1"     
## [13] "ENTPD1-AS1"     "SLC8A1-AS1"     "RP11-202G18.1"  "HCG22"         
## [17] "CCDC26"         "RP11-142M10.2"  "LINC00884"      "RNASEH2B-AS1"  
## [21] "RP11-353M9.1"   "CCDC200"        "RP11-360F5.1"   "LINC02057"     
## [25] "LINC01258"      "RP11-238K6.1"   "RP11-624C23.1"  "RP11-452H21.1" 
## [29] "SMIM35"         "RP11-196H14.2"  "RP11-136F16.1"  "LINC00621"     
## [33] "CEACAM16-AS1"   "RP11-399K21.11" "LINC02712"      "RP11-323P17.2" 
## [37] "RP11-264E23.4"  "RP11-13J12.3"  
## [1] "found 11 genes."

## [1] 13
##  [1] "ATP8B1"         "SLC5A9"         "SGCE"           "PDE5A"         
##  [5] "ENO4"           "FAM177B"        "INSYN2B"        "ANKUB1"        
##  [9] "AC002463.3"     "ARHGAP26-AS1"   "AC017101.10"    "AC096558.1"    
## [13] "SRGAP2-AS1"     "AC083884.8"     "AC037445.1"     "RP11-666F17.1" 
## [17] "CPB2-AS1"       "MYCBP2-AS1"     "DIAPH2-AS1"     "AC018890.6"    
## [21] "CTD-2015H6.3"   "CTD-2227I18.1"  "RHOQ-AS1"       "RP11-649G15.2" 
## [25] "AP000487.6"     "RP11-513G19.1"  "USP3-AS1"       "RP11-815J21.4" 
## [29] "RP11-16B9.1"    "ABHD15-AS1"     "RP11-16C1.3"    "RP11-793A3.2"  
## [33] "RP11-53B2.3"    "CTD-2282P23.2"  "RP11-793H13.14" "DISC2"         
## [37] "RP11-65F13.4"   "RP11-1146N6.3"  "AC009505.4"    
## [1] "found 8 genes."

## [1] 14
##  [1] "ZFP64"          "NEXMIF"         "CASS4"          "PITPNM2"       
##  [5] "PLCL1"          "BEX1"           "RALGPS1"        "GPAT3"         
##  [9] "RAB40B"         "NRGN"           "TSPAN7"         "PLXDC1"        
## [13] "SMIM14"         "NXN"            "MIR31HG"        "MACROD2"       
## [17] "FIGN"           "LIPE-AS1"       "ALOX12-AS1"     "KIF9-AS1"      
## [21] "RP11-120D5.1"   "RP11-246A10.1"  "MRPS30-DT"      "RP11-370I10.6" 
## [25] "LINC01572"      "RP11-495L19.1"  "TENM1"          "ADGRL1"        
## [29] "GDF11"          "PLXNC1"         "CFAP161"        "ST3GAL2"       
## [33] "CXXC5"          "CDH4"           "ANKS1B"         "CTD-3088G3.8"  
## [37] "SYCP2"          "RORB"           "LL22NC03-2H8.5"
## [1] "found 27 genes."

## [1] 15
##  [1] "ADAM28"      "ST6GAL1"     "IPCEF1"      "PLAT"        "IGSF21"     
##  [6] "RCAN3"       "PLAU"        "ITPR2"       "ABCC4"       "C3"         
## [11] "FOXP2"       "LYVE1"       "GARNL3"      "GIPC2"       "GAREM1"     
## [16] "AIG1"        "FRMD4A"      "PRMT9"       "CX3CR1"      "P2RY12"     
## [21] "LRRC8C"      "CA8"         "SLC9A9"      "CH17-55D9.1" "ARHGAP15"   
## [26] "SLC1A3"      "IL27RA"      "LIFR"        "FOXP1"       "OGFRL1"     
## [31] "SLC41A2"     "CSGALNACT1"  "JAZF1"       "MTSS1"       "BNC2"       
## [36] "MAML2"       "IFNLR1"     
## [1] "found 36 genes."

## [1] 16
##  [1] "HIVEP2"        "SLC9A7"        "HDHD5"         "MAP3K20"      
##  [5] "ARRDC2"        "AK1"           "STN1"          "MXI1"         
##  [9] "GTDC1"         "ATP8A1"        "CEMIP2"        "RASGEF1B"     
## [13] "PGGHG"         "ST18"          "SLC26A7"       "ZFYVE28"      
## [17] "KLF13"         "RESF1"         "LPCAT4"        "RBM44"        
## [21] "TMTC2"         "TNFAIP8L3"     "NCMAP"         "ZNF395"       
## [25] "TPRG1"         "ERO1A"         "LINC02397"     "AS3MT"        
## [29] "FAM229A"       "SGO1-AS1"      "DIRC3"         "DARS1-AS1"    
## [33] "LINC01762"     "AF064858.8"    "RP11-305L7.3"  "FMNL1-DT"     
## [37] "LINC01138"     "MYOCOS"        "RP11-344F5.1"  "RP11-249L21.6"
## [1] "found 29 genes."

## [1] 17
##  [1] "MMP24"         "GLIPR1L1"      "EYS"           "FSIP2"        
##  [5] "SPDYE2"        "HDAC4-AS1"     "ELMO1-AS1"     "TMLHE-AS1"    
##  [9] "HNRNPA1P48"    "LINC01375"     "AC105461.1"    "RP11-165F24.3"
## [13] "RP11-526K17.2" "ALG13-AS1"     "RP1-225E12.2"  "COA6-AS1"     
## [17] "RP11-528G1.2"  "RP11-575L7.8"  "BCL2L1-AS1"    "DENND6A-AS1"  
## [21] "ZBTB20-AS5"    "LINC00960"     "RP11-712B9.2"  "MEF2C-AS2"    
## [25] "RP11-268P4.5"  "RP11-39E3.3"   "RP11-506H20.1" "RP11-434H14.1"
## [29] "RP11-370I10.2" "CTD-2647E9.3"  "RP11-317G6.1"  "RP11-703M24.5"
## [33] "CTD-3149D2.4"  "RP4-769N13.7"  "RP1-256G22.2"  "RP11-121C2.3" 
## [37] "RP11-7F3.1"    "RP11-685G9.5"  "RP11-555K12.4" "RP11-56I23.2" 
## [1] "found 5 genes."

## [1] 18
##  [1] "ZFY"                     "SLC26A3"                
##  [3] "PCDH11Y"                 "PXDNL"                  
##  [5] "NR6A1"                   "SEMA3E"                 
##  [7] "FUT10"                   "LRRC3B"                 
##  [9] "CCDC73"                  "POTEG"                  
## [11] "RP11-37N22.1"            "AC023469.1"             
## [13] "AC067959.1"              "RP11-147G16.1"          
## [15] "RP11-154D17.1"           "MYO16-AS1"              
## [17] "AC013463.2"              "LINC02646"              
## [19] "AC002066.1"              "CTD-2643I7.5"           
## [21] "RP11-696N14.1"           "RP11-17A1.3"            
## [23] "RP11-259O2.1"            "RP11-79E3.2"            
## [25] "LINC01609"               "RP11-351A11.1"          
## [27] "RP11-13N12.1"            "RP11-20D14.3"           
## [29] "MTRNR2L12"               "RMRP_ENSG00000269900"   
## [31] "SCARNA2_ENSG00000270066" "AGBL1"                  
## [33] "CH507-513H4.1"           "CH507-528H12.1"         
## [35] "RP11-596C23.6"           "RP4-799O8.1"            
## [37] "RP11-322M13.1"           "AC003099.2"             
## [39] "RP11-398J12.1"           "RP11-404C6.6"           
## [1] "found 12 genes."

## [1] 19
##  [1] "RPL3"          "RPL18A"        "RPL19"         "RPL34"        
##  [5] "RPL24"         "FGF13"         "MTHFS"         "RPS24"        
##  [9] "PRDM5"         "RPS2"          "RPS11"         "RPL11"        
## [13] "SPAG16"        "RPL32"         "FAU"           "ATG10"        
## [17] "RPL26"         "ELAVL4"        "MRPL1"         "RPL38"        
## [21] "RPLP2"         "RPS23"         "SPATS2L"       "CPNE4"        
## [25] "RPL12"         "RPL23A"        "RPL39"         "AIF1"         
## [29] "RP11-535M15.1" "LINC01278"     "PVT1"          "RP11-37B2.1"  
## [33] "SLC1A2"        "LPL"           "ADARB1"        "LILRB3"       
## [1] "found 32 genes."

## [1] 20
##  [1] "STS"        "MID1"       "CCDC170"    "DOCK10"     "IRF8"      
##  [6] "ITGA9"      "AC097721.2" "XIST"       "TWIST2"     "MEI4"      
## [11] "SCIN"       "LCP2"       "CTTNBP2"    "DOCK9"      "IRAK3"     
## [16] "INTS6"      "NCOA7"      "TSHZ3"      "PTPRE"      "PRAM1"     
## [21] "CCNH"       "FAM13A"     "SSH2"       "USP53"      "SDK1"      
## [26] "DIXDC1"     "FER"        "ACSL1"      "MERTK"      "GPHN"      
## [31] "CHD2"       "CMSS1"      "GPRIN3"     "MITF"       "RALGAPA2"  
## [36] "PLCG2"     
## [1] "found 34 genes."

## [1] 21
##  [1] "MPP2"     "ATF5"     "FGR"      "LRRC7"    "CDK14"    "CDK17"   
##  [7] "ARHGAP10" "IGSF9B"   "ITPKC"    "HIVEP1"   "FGF14"    "POU6F2"  
## [13] "CPE"      "MOB3B"    "RAMP1"    "MACROD1"  "PDZD2"    "CNKSR2"  
## [19] "ADGRL3"   "LONRF1"   "NCAM2"    "SORCS3"   "GMEB1"    "CSMD3"   
## [25] "CRADD"    "NLGN1"    "CTNND2"   "PTGER4"   "NEGR1"    "CNTNAP2" 
## [31] "CADM2"    "ZBTB7A"   "NRXN1"    "ZBTB7C"   "LSAMP"    "NRG3"    
## [37] "SNHG14"  
## [1] "found 36 genes."

## [1] 22
##  [1] "ICA1"         "MCF2L2"       "IL1A"         "ZRANB3"       "EFCAB11"     
##  [6] "TCERG1L"      "KCNMB2"       "CTA-292E10.6" "LINC00996"    "KCNQ1OT1"    
## [11] "AC009166.9"   "CNTN1"        "NCDN"         "HPCAL4"       "SLC2A5"      
## [16] "CACNA1B"      "CACNA1C"      "SCN3A"        "CACNA2D1"     "PTPRN2"      
## [21] "SYN2"         "SPTBN4"       "EDIL3"        "RBFOX3"       "GRM5"        
## [26] "KCND3"        "DPP10"        "MSRA"         "PCDH9"        "KCND2"       
## [31] "PRKG1"        "SYN3"         "GRM7"         "FAM153CP"     "U91319.1"    
## [1] "found 29 genes."

## [1] 23
##  [1] "CEACAM1"       "SLC9B1"        "RP11-281P23.2" "RP11-493L12.3"
##  [5] "RP11-516C1.1"  "CELSR3"        "ABCA7"         "PLEKHH3"      
##  [9] "ANO8"          "MLF2"          "GALNT16"       "HELLS"        
## [13] "TGFBI"         "HIF3A"         "CHI3L1"        "FGF17"        
## [17] "LYPD5"         "TNFRSF11B"     "ADCY5"         "H2AC6"        
## [21] "VMO1"          "NHEJ1"         "EME2"          "ZNF521"       
## [25] "ZDBF2"         "AF064858.6"    "SLC12A8"       "RP11-384C4.7" 
## [29] "RP3-467L1.4"   "RP11-657O9.1"  "ARHGEF25"      "LINC01414"    
## [33] "RP11-661A12.5" "MTRNR2L1"      "RP11-429A20.3" "RP11-81K2.1"  
## [37] "LINC00551"    
## [1] "found 25 genes."

## [1] 24
##  [1] "ZDHHC19"       "RP11-713N11.4" "PKD1"          "SLC2A3"       
##  [5] "DDX3Y"         "HACE1"         "PPP1R15A"      "GADD45B"      
##  [9] "RNMT"          "FLT1"          "IL4I1"         "APBB3"        
## [13] "USP9Y"         "SPP1"          "SRGN"          "TREM1"        
## [17] "MICAL2"        "RGS16"         "MYO10"         "PLIN2"        
## [21] "TAMALIN"       "ALDH1A1"       "DDIT4"         "FAM210A"      
## [25] "ADSS1"         "ANKRD37"       "IARS1"         "H2BU1"        
## [29] "CEBPD"         "ZSCAN31"       "HIF1A-AS3"     "CTD-2285E13.1"
## [33] "RP11-134L10.2"
## [1] "found 28 genes."

## [1] 25
##  [1] "CALCR"         "IL7"           "NEURL2"        "PIGC"         
##  [5] "ADGRA3"        "ADGRG5"        "RNF180"        "LINC00476"    
##  [9] "IRAG1-AS1"     "CATSPERE"      "SDHAF3"        "SCOC-AS1"     
## [13] "PAPSS2"        "CARNMT1-AS1"   "ATP6AP1L"      "ENTPD3-AS1"   
## [17] "TMEM72-AS1"    "TSBP1-AS1"     "RP13-188A5.1"  "RP5-1198O20.4"
## [21] "FSIP2-AS1"     "IPO9-AS1"      "UFL1-AS1"      "RPL34-DT"     
## [25] "RP11-195C7.1"  "LRIG2-DT"      "LINC01877"     "RORA-AS1"     
## [29] "STX18-AS1"     "RP11-130F10.1" "LIX1-AS1"      "DISC1FP1"     
## [33] "RP11-160E2.6"  "RP11-74J13.8"  "EIF1B-AS1"     "RP11-736I24.5"
## [37] "RP11-19D22.1"  "RP11-622O11.6" "RP11-261A24.1" "RP11-237N2.1" 
## [41] "RP1-236J16.3"  "RP11-120L14.1"
## [1] "found 10 genes."

## [1] 26
##  [1] "ERCC8"         "DHRS9"         "ANGPT2"        "CHN1"         
##  [5] "UBE2Q2"        "BCL2A1"        "TNFRSF21"      "IRAK1BP1"     
##  [9] "TEX9"          "ABCA5"         "PAQR3"         "LCLAT1"       
## [13] "RP11-131L23.1" "RPL41"         "VCAN"          "KCNAB2"       
## [17] "MYOM1"         "KATNAL1"       "SPOCK2"        "SLC16A10"     
## [21] "GABRG2"        "CYTIP"         "HIP1"          "BTG1"         
## [25] "PITPNC1"       "RASA2"         "ZMAT4"         "OTUD1"        
## [29] "ATOH8"         "C11orf80"      "MCTP1"         "JAKMIP2"      
## [33] "CD247"         "TOX"           "MIR155HG"      "LUCAT1"       
## [37] "RP11-475M20.2"
## [1] "found 33 genes."

## [1] 27
##  [1] "DERA"     "TDRD3"    "DAAM1"    "GDAP1"    "ARSB"     "EPHB2"   
##  [7] "STAMBPL1" "NUBPL"    "NFIA"     "KIF26B"   "ARHGAP25" "DYNC2H1" 
## [13] "CCDC7"    "CLEC16A"  "LIMCH1"   "RFX3"     "PHLPP1"   "RFX2"    
## [19] "TRPS1"    "PRKAG2"   "SASH1"    "ELL2"     "IQSEC2"   "IQSEC1"  
## [25] "FARP1"    "MSI2"     "RBM47"    "SLC43A2"  "DHRSX"    "AFF1"    
## [31] "PACS1"    "SAMD12"   "SERTAD2"  "GDI1"    
## [1] "found 34 genes."

## [1] 28
##  [1] "RIPOR2"        "DUOX1"         "MCTP2"         "TMEM44"       
##  [5] "LINC00467"     "BEX3"          "RAB37"         "H2BC4"        
##  [9] "H2AC20"        "MTCP1"         "GOLGA8B"       "AC023590.1"   
## [13] "ZNF451-AS1"    "WEE2-AS1"      "PCDH9-AS2"     "RP11-142A5.1" 
## [17] "KCNMA1-AS1"    "RP11-544A12.4" "RP5-1101C3.1"  "RP11-115J16.1"
## [21] "RP11-120A1.1"  "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"  
## [25] "TCF4-AS1"      "RP11-126O1.4"  "TSIX"          "H2AC19"       
## [29] "RP11-386I14.4" "H2BC8"         "H2AC8"         "H2BC7"        
## [33] "TRG-AS1"       "RP11-275G7.2"  "GS1-98E2.1"    "RP11-21M24.6" 
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"       
## [1] "found 15 genes."

## [1] 29
##  [1] "CD74"          "CST3"          "OGN"           "SLC2A9"       
##  [5] "FLVCR2"        "XAF1"          "ITM2C"         "SMAD6"        
##  [9] "PTH2R"         "LY96"          "COPG2"         "C1QC"         
## [13] "S100Z"         "C1QB"          "RTTN"          "PROS1"        
## [17] "CHSY3"         "FIRRE"         "LINC00894"     "RP11-574F11.4"
## [21] "TRHDE"         "RASSF2"        "MAN1A1"        "FRMD4B"       
## [25] "COL5A1"        "CHSY1"         "TLR2"          "NGLY1"        
## [29] "CDCP1"         "NPTX1"         "LRFN4"         "TLR5"         
## [33] "PELI1"         "GK"            "ZNF277"        "UBXN2B"       
## [37] "ZNF407"       
## [1] "found 34 genes."

## [1] 30
##  [1] "PRDM11"        "CFAP74"        "RTN4RL1"       "KCNT1"        
##  [5] "BICRAL"        "SEMA6D"        "ZNF365"        "RBMS3"        
##  [9] "NPAS3"         "SPOCK1"        "CFAP251"       "CAMK2N1"      
## [13] "GABRB1"        "LRFN5"         "PDZRN4"        "HTR1E"        
## [17] "GPC5"          "KCTD16"        "GLDN"          "PTPRT"        
## [21] "NPIPB15"       "ZNF846"        "TAFA2"         "FAM155A"      
## [25] "MEG3"          "MIAT"          "RP5-864K19.4"  "ARL17B"       
## [29] "SHISA9"        "RP11-111A21.1" "RP11-707P17.1" "RP11-368L12.1"
## [33] "RP11-396B14.2" "IQCJ-SCHIP1"   "RP11-114N19.3" "RP11-358F13.1"
## [37] "RP11-335E8.3"  "RP11-452F19.4"
## [1] "found 26 genes."

## [1] 31
##  [1] "TTC7A"         "SP140"         "ARHGEF18"      "TMEM241"      
##  [5] "ARL5C"         "BEND6"         "ENPP3"         "C4orf19"      
##  [9] "MAMDC2"        "LIPC"          "ZMAT3"         "MARCHF3"      
## [13] "SCFD2"         "CDIN1"         "KBTBD12"       "LINC01356"    
## [17] "LINC01357"     "LINC00539"     "AC105760.2"    "LINC01141"    
## [21] "LINC01684"     "KCNMB2-AS1"    "ARHGAP8"       "XACT"         
## [25] "PTCHD4"        "LINC00968"     "MEF2C-AS1"     "RP11-541P9.3" 
## [29] "ZNF10"         "RP11-630C16.2" "RP11-493L12.4" "LINC00907"    
## [33] "ATP6V0D1-DT"   "RP11-437L7.2"  "RP11-111G13.1" "RP4-545L17.11"
## [37] "RP11-168F24.3" "STAB1"         "AC025171.1"    "CTB-41I6.2"   
## [1] "found 19 genes."

## [1] 32
##  [1] "ZNF532"       "OPHN1"        "PIGL"         "MS4A4A"       "TENT5A"      
##  [6] "LDAH"         "MTERF1"       "PUDP"         "SLC49A4"      "FBN2"        
## [11] "WDPCP"        "PID1"         "CLIC2"        "RAB28"        "NMNAT3"      
## [16] "TMEM144"      "CCDC171"      "ACYP2"        "FGGY"         "WDR25"       
## [21] "PCED1B"       "RNLS"         "B3GLCT"       "LINC01285"    "PRDX6-AS1"   
## [26] "ZNF433-AS1"   "FTCDNL1"      "SLC16A1-AS1"  "TEX41"        "ZRANB2-AS2"  
## [31] "RFX3-AS1"     "LINC01376"    "LINC01184"    "RP11-319G6.1" "CTB-161M19.4"
## [36] "C8orf37-AS1"  "PRANCR"       "LINC01146"    "MMP28"        "RP1-111C20.3"
## [1] "found 25 genes."

## [1] 33
##  [1] "OSBPL6"   "PDE4D"    "RALGPS2"  "RFC3"     "PIGK"     "MAGI1"   
##  [7] "PTPN14"   "SETBP1"   "TIAM1"    "PLEKHA7"  "ATAD5"    "DNAH14"  
## [13] "WWC3"     "PLEKHA5"  "PDE4A"    "CUX2"     "RLF"      "ESYT2"   
## [19] "DENND1A"  "MAPK8IP1" "STARD13"  "AGAP3"    "DENND4C"  "WDR45B"  
## [25] "RIT2"     "SRSF12"   "AGAP1"    "FAM110B"  "ROBO1"    "TANC2"   
## [31] "FAM20C"   "CADM1"    "PDE4B"    "SIPA1L1"  "RGL3"    
## [1] "found 35 genes."

## [1] 34
##  [1] "TXNDC16"                 "PCSK1N"                 
##  [3] "LRRC6"                   "CALY"                   
##  [5] "LPAR6"                   "UNC80"                  
##  [7] "GPR85"                   "SKA2"                   
##  [9] "ERC2"                    "COL5A2"                 
## [11] "AC011288.2"              "ALG1L9P_ENSG00000248671"
## [13] "CTD-2537O9.1"            "CEROX1"                 
## [15] "RP11-305E17.8"           "COPG2IT1"               
## [17] "ADAM22"                  "RAPGEF4"                
## [19] "ANKRD12"                 "RAPGEF1"                
## [21] "PPFIA2"                  "CDH18"                  
## [23] "FMN2"                    "FMNL2"                  
## [25] "CLASP2"                  "OXR1"                   
## [27] "LRP1B"                   "DLGAP1"                 
## [29] "RIMS2"                   "CSMD1"                  
## [31] "OPCML"                   "RALYL"                  
## [33] "KCNIP4"                  "MYT1L"                  
## [35] "MAGI2"                   "COL27A1"                
## [37] "NEAT1"                   "SAP30-DT"               
## [1] "found 29 genes."

## [1] 35
##  [1] "PRKCQ"        "MTHFD2L"      "PRKCH"        "ARAP2"        "ZFAT"        
##  [6] "MYO9A"        "SESN1"        "ZNF586"       "DOCK3"        "DCUN1D4"     
## [11] "WNT2B"        "RGL1"         "CAMKMT"       "AMN1"         "RASGRP3"     
## [16] "AGPAT5"       "ADK"          "CDC42SE2"     "EPB41"        "STARD9"      
## [21] "NEK10"        "RNF150"       "MALT1"        "SLC35E3"      "ZHX2"        
## [26] "AIDA"         "ARL4C"        "CARD11"       "LINC00862"    "DENND1B"     
## [31] "C17orf67"     "SOGA3"        "KLF3-AS1"     "AC092835.2"   "RP1-179N16.6"
## [36] "SELENOP"      "HCG17"        "C2orf27A"    
## [1] "found 32 genes."

## [1] 36
##  [1] "MBNL3"         "P3H2"          "APBA1"         "GCNT2"        
##  [5] "PEX7"          "AKAP7"         "SLC10A7"       "RAB38"        
##  [9] "DTD1"          "METTL25"       "LANCL2"        "DPH6"         
## [13] "ARHGAP20"      "ARMH4"         "LRIG1"         "CD226"        
## [17] "MAP3K7CL"      "TNFRSF13C"     "PUS10"         "MBOAT1"       
## [21] "CAPS2"         "LEKR1"         "LIN52"         "LINC00630"    
## [25] "RP11-162D16.2" "MIR646HG"      "C12orf75"      "RP11-381K20.2"
## [29] "LINC02762"     "GMDS-DT"       "RP11-679C8.2"  "LINC02328"    
## [33] "RP11-323I15.5" "KLHL24"        "SLC35E1"       "IL15"         
## [37] "TMEM65"       
## [1] "found 28 genes."

## [1] 37
##  [1] "SLC26A4"    "PLGRKT"     "MAP3K8"     "PLEK"       "CENPK"     
##  [6] "MIS18BP1"   "SAT1"       "ZSCAN5A"    "PCBD2"      "EPSTI1"    
## [11] "AHI1"       "SLC22A23"   "BCAS3"      "TRPC1"      "SLC25A25"  
## [16] "C11orf49"   "PSTPIP2"    "CACNA1D"    "BTG2"       "ANO10"     
## [21] "CDYL2"      "PBX3"       "XKR6"       "MX2"        "APOO"      
## [26] "KIAA0825"   "ZFP36L1"    "SRGAP3"     "CDKN2B-AS1" "JARID2"    
## [31] "MSR1"       "CTNNA2"     "UBE2R2"     "MGAT1"      "RNF144B"   
## [36] "TNFAIP8"    "RASSF3"     "ACOT11"    
## [1] "found 36 genes."

## [1] 38
##  [1] "SNCAIP"  "RPH3A"   "LRRC74A" "MEIS1"   "RORA"    "RAB27A"  "SMARCD3"
##  [8] "CELF4"   "TBL1X"   "NPDC1"   "EPHA4"   "AKT3"    "EMILIN2" "DRAM1"  
## [15] "KCNH1"   "PAM"     "CLVS2"   "LRRC4C"  "CLEC1A"  "CRIM1"   "PDE3B"  
## [22] "KALRN"   "ZFPM2"   "PPM1E"   "ALOX15B" "ZDHHC20" "UNC5C"   "TSHZ2"  
## [29] "EFNA5"   "NELL2"   "OSBP2"   "PBX1"    "KAZN"    "MIB2"    "MICAL3" 
## [36] "GRIN2B" 
## [1] "found 36 genes."

## [1] 39
##  [1] "PKD2L2"        "ANGPTL1"       "CYREN"         "ATP5F1E"      
##  [5] "OMD"           "ACKR4"         "IER3"          "AGBL3"        
##  [9] "C11orf65"      "CYTL1"         "DNAJC24"       "RP11-321C24.1"
## [13] "RP4-568F9.6"   "ARHGAP15-AS1"  "RAP2C-AS1"     "LANCL1-AS1"   
## [17] "ITGA9-AS1"     "FBXO30-DT"     "RP11-123B3.2"  "RP1-117O3.2"  
## [21] "KDM4A-AS1"     "RP11-775D22.3" "RP11-796E2.4"  "RP11-544A12.8"
## [25] "ANK2-AS1"      "FAM198B-AS1"   "AC006160.5"    "CTD-3239E11.2"
## [29] "RP11-1H15.2"   "RP11-571M6.7"  "RP11-638I2.8"  "RP11-66H6.3"  
## [33] "PRKCA-AS1"     "RP11-737O24.2" "RP11-622I12.1" "RP11-458A7.1" 
## [37] "RP1-80B9.4"    "RP11-1H15.4"   "RP1-18C9.3"    "RP11-6G22.1"  
## [41] "CTD-2021K4.2" 
## [1] "found 11 genes."

## [1] 40
##  [1] "ARSJ"          "LINC00639"     "RP11-617F9.2"  "MAMLD1"       
##  [5] "RASGRP2"       "COL5A3"        "LILRB5"        "HS3ST2"       
##  [9] "OLFM1"         "PATJ"          "BTBD11"        "ME3"          
## [13] "FBXO32"        "PALM2AKAP2"    "NRG2"          "JAML"         
## [17] "PLPP3"         "SNED1"         "PRICKLE2"      "ARHGEF3"      
## [21] "STXBP6"        "TBC1D10C"      "ADGRB1"        "H1-10"        
## [25] "SLIT1"         "LINC00910"     "CR1L"          "LINC00970"    
## [29] "XKR9"          "LINC01320"     "SATB1-AS1"     "LIMD1-AS1"    
## [33] "RP11-47I22.3"  "CYP1B1-AS1"    "TRHDE-AS1"     "LINC01322"    
## [37] "USP2-AS1"      "CPEB2-DT"      "RP5-1015P16.1" "RENO1"        
## [1] "found 24 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4168494 222.7   10243768 547.1         NA 10243768 547.1
## Vcells 8941231  68.3   29538339 225.4      65536 29538339 225.4

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5